The game was written by Yoko, Haha Kikuchi and Yoshiho Akabane. The team defined the game's central theme as "agaku", a Japanese word meaning to struggle out of a bad situation. Another theme for the game was "love", which was unusual given that all the central cast were robots, which were not normally associated with emotions.

According to Yoko, while the scenario of Nier was "wet" in its emotional content, for Nier: Automata he aimed for a "dry" narrative concerning the world's inherent unfairness and the prejudices the characters are forced to confront.